skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Molecular basis for the role of oncogenic histone mutations in modulating H3K36 methylation

Journal Article · · Scientific Reports
DOI:https://doi.org/10.1038/srep43906· OSTI ID:1355913

Histone H3 lysine 36 methylation (H3K36me) is critical for epigenetic regulation and mutations at or near H3K36 are associated with distinct types of cancers. H3K36M dominantly inhibits H3K36me on wild-type histones, whereas H3G34R/V selectively affects H3K36me on the same histone tail. Here we report the crystal structures of SETD2 SET domain in complex with an H3K36M peptide and SAM or SAH. There are large conformational changes in the substrate binding regions of the SET domain, and the K36M residue interacts with the catalytic pocket of SETD2. H3G34 is surrounded by a very narrow tunnel, which excludes larger amino acid side chains. H3P38 is in the trans configuration, and the cis configuration is incompatible with SETD2 binding. Lastly, mutations of H3G34 or H3P38 alleviate the inhibitory effects of H3K36M on H3K36me, demonstrating that the stable interaction of H3K36M with SETD2 is critical for its inhibitory effects.

Research Organization:
Columbia Univ., New York, NY (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1355913
Journal Information:
Scientific Reports, Vol. 7; ISSN 2045-2322
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 42 works
Citation information provided by
Web of Science

References (31)

The Language of Histone Crosstalk journal September 2010
Understanding the language of Lys36 methylation at histone H3 journal January 2012
Histone H3 mutations—a special role for H3.3 in tumorigenesis? journal March 2015
Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma journal January 2012
Hotspot Mutations in H3F3A and IDH1 Define Distinct Epigenetic and Biological Subgroups of Glioblastoma journal October 2012
Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone journal October 2013
The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression journal April 2013
A lesson learned from the H3.3K27M mutation found in pediatric glioma: A new approach to the study of the function of histone modifications in vivo? journal August 2013
Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma journal March 2013
The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas journal May 2016
Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape journal May 2016
Proline Isomerization of Histone H3 Regulates Lysine Methylation and Gene Expression journal September 2006
A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading journal September 2016
Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling journal August 2014
Reduced H3K27me3 and DNA Hypomethylation Are Major Drivers of Gene Expression in K27M Mutant Pediatric High-Grade Gliomas journal November 2013
S -adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3 journal May 2016
Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2 journal April 2016
Structural Biology of Human H3K9 Methyltransferases journal January 2010
Sinefungin Derivatives as Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2 journal October 2012
Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase journal July 2016
Centromere Silencing and Function in Fission Yeast Is Governed by the Amino Terminus of Histone H3 journal October 2003
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
Phaser crystallographic software journal July 2007
PHENIX : building new software for automated crystallographic structure determination journal October 2002
The Target of the NSD Family of Histone Lysine Methyltransferases Depends on the Nature of the Substrate journal October 2009
Crystal Structure of the Human Histone Methyltransferase ASH1L Catalytic Domain and Its Implications for the Regulatory Mechanism journal January 2011
The Structure of NSD1 Reveals an Autoregulatory Mechanism Underlying Histone H3K36 Methylation journal December 2010
Heterogeneous Nuclear Ribonucleoprotein L Is a Subunit of Human KMT3a/Set2 Complex Required for H3 Lys-36 Trimethylation Activity in Vivo journal March 2009
Coot model-building tools for molecular graphics journal November 2004
Histone H3 K36 Methylation Is Associated with Transcription Elongation in Schizosaccharomyces pombe journal August 2005
Set2 Is a Nucleosomal Histone H3-Selective Methyltransferase That Mediates Transcriptional Repression journal March 2002

Cited By (8)

Mutation-driven epigenetic alterations as a defining hallmark of central cartilaginous tumours, giant cell tumour of bone and chondroblastoma journal November 2019
Nucleosome and ubiquitin position Set2 to methylate H3K36 journal August 2019
Recognition of cancer mutations in histone H3K36 by epigenetic writers and readers journal July 2018
Invited Review: Emerging functions of histone H3 mutations in paediatric diffuse high‐grade gliomas journal January 2020
Emerging roles of telomeric chromatin alterations in cancer journal January 2019
Identification of a peptide inhibitor for the histone methyltransferase WHSC1 journal May 2018
Histone H3 Mutations: An Updated View of Their Role in Chromatin Deregulation and Cancer journal May 2019
Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe journal July 2017